crossing96/oncoscreening huggingface dataset:
Transcriptome sequencing identifies ANLN as a promising prognostic biomarker in bladder urothelial carcinoma.	The prognosis of bladder urothelial carcinoma (BLCA) varies greatly even for patients with similar pathological characteristics. We conducted transcriptome sequencing on ten pairs of BLCA samples and adjacent normal tissues to identify differentially expressed genes. Anillin (ANLN) was identified as a transcript that was significantly up-regulated in BLCA samples compared with normal tissues. Prognostic power of candidate gene was studied using qRT-PCR and immunohistochemistry on 40 and 209 patients, respectively. Patients with elevated ANLN expression level was correlated with poorer cancer-specific (median, 22.4 vs. 37.3 months, p = 0.001), progression-free (median, 19.7 vs. 27.9 months, p = 0.001) and recurrence-free survival (median, 17.1 vs. 25.2 months, p = 0.011) compared with low ANLN expression. Public datasets TCGA and NCBI-GEO were analyzed for external validation. Knockdown of ANLN in J82 and 5637 cells using small interfering RNA significantly inhibited cell proliferation, migration, and invasion ability. Moreover, knockdown of ANLN resulted in G2/M phase arrest and decreased expression of cyclin B1 and D1. Microarray analysis suggested that ANLN played a major role in cell migration and was closely associated with several cancer-related signaling pathways. In conclusion, ANLN was identified as a promising prognostic biomarker which could be used to stratify different risks of BLCA.	bladder
Centralisation of radical cystectomies for bladder cancer in England, a decade on from the 'Improving Outcomes Guidance': the case for super centralisation.	OBJECTIVE: To analyse the impact of centralisation of radical cystectomy (RC) provision for bladder cancer in England, on postoperative mortality, length of stay (LoS), complications and re-intervention rates, from implementation of centralisation from 2003 until 2014. In 2002, UK policymakers introduced the 'Improving Outcomes Guidance' (IOG) for urological cancers after a global cancer surgery commission identified substantial shortcomings in provision of care of RCs. One key recommendation was centralisation of RCs to high-output centres. No study has yet robustly analysed the changes since the introduction of the IOG, to assess a national healthcare system that has mature data on such institutional transformation. PATIENTS AND METHODS: RCs performed for bladder cancer in England between 2003/2004 and 2013/2014 were analysed from Hospital Episode Statistics (HES) data. Outcomes including 30-day, 90-day, and 1-year all-cause postoperative mortality; median LoS; complication and re-intervention rates, were calculated. Multivariable statistical analysis was undertaken to describe the relationship between each surgeon and the providers' annual case volume and mortality. RESULTS: In all, 15 292 RCs were identified. The percentage of RCs performed in discordance with the IOG guidelines reduced from 65% to 12.4%, corresponding with an improvement in 30-day mortality from 2.7% to 1.5% (P = 0.024). Procedures adhering to the IOG guidelines had better 30-day mortality (2.1% vs 2.9%; P = 0.003) than those that did not, and better 1-year mortality (21.5% vs 25.6%; P < 0.001), LoS (14 vs 16 days; P < 0.001), and re- intervention rates (30.0% vs 33.6%; P < 0.001). Each single extra surgery per centre reduced the odds of death at 30 days by 1.5% (odds ratio [OR] 0.985, 95% confidence interval [CI] 0.977-0.992) and 1% at 1 year (OR 0.990, 95% CI 0.988-0.993), and significantly reduced rates of re-intervention. CONCLUSION: Centralisation has been implemented across England since the publication of the IOG guidelines in 2002. The improved outcomes shown, including that a single extra procedure per year per centre can significantly reduce mortality and re-intervention, may serve to offer healthcare planners an evidence base to propose new guidance for further optimisation of surgical provision, and hope for other healthcare systems that such widespread institutional change is achievable and positive.	bladder
SLC14A1: a novel target for human urothelial cancer.	Urinary bladder cancer is the second commonly diagnosed genitourinary malignancy. Previously, bio-molecular alterations have been observed within certain locations such as chromosome 9, retinoblastoma gene and fibroblast growth factor receptor-3. Solute carrier family 14 member 1 (SLC14A1) gene encodes the type-B urea transporter (UT-B) which facilitates the passive movement of urea across cell membrane, and has recently been related with human malignancies, especially for bladder cancer. Herein, we discussed the SLC14A1 gene and UT-B protein properties, aiming to elucidate the expression behavior of SLC14A1 in human bladder cancer. Furthermore, by reviewing some well-established theories regarding the carcinogenesis of bladder cancer, including several genome wide association researches, we have bridged the mechanisms of cancer development with the aberrant expression of SLC14A1. In conclusion, the altered expression of SLC14A1 gene in human urothelial cancer may implicate its significance as a novel target for research.	bladder
Non-invasive papillary urothelial carcinoma of the vagina: molecular analysis of a rare case identifies clonal relationship to non-invasive urothelial carcinoma of the bladder.	"We present a rare case of non-invasive papillary urothelial carcinoma of the vagina as the initial presentation of a multicentric urothelial carcinoma also involving bladder and renal pelvis and report for the first time in the literature the molecular alterations observed in the vaginal urothelial lesion and the synchronous lesions of the urinary tract. In this case, the non-invasive papillary urothelial carcinoma in the vagina displayed the same genetic alterations in the FGFR3 and PIK3CA genes as those seen in the non-invasive papillary urothelial carcinoma of the bladder contrasting with the wild phenotype observed in the invasive urothelial carcinoma of the renal pelvis. This observation could reinforce the theory of ""seeding"" of carcinoma cells as a valid and most likely explanation of this multifocality. In addition, we emphasize in this report the importance of recognizing this rare lesion in the female genital tract and its differential diagnosis."	bladder
Comparisons of Quality of Life and Functional and Oncological Outcomes after Orthotopic Neobladder Reconstruction: Prostate-Sparing Cystectomy versus Conventional Radical Cystoprostatectomy.	OBJECTIVES: To compare health-related quality of life and oncological and functional outcomes on erectile function, continence, and voiding function among bladder patients who underwent orthotopic neobladder reconstruction after prostate-sparing cystectomy (PSC) and conventional radical cystoprostatectomy (CRC). METHODS: This is a retrospective cohort study from a single surgeon. During 2007 to 2015, we identified 25 of 186 male patients receiving radical cystectomies due to bladder cancer who underwent orthotopic neobladder reconstruction, 14 patients with PSC and the other 11 patients with CRC. International Index of Erectile Function-5 (IIEF-5), International Prostate Symptom Score (IPSS), European Organization for Research and Treatment of Cancer-Quality of Life Questionnaire-Core 30-item questionnaire (EORTC-QLQ-C30), and self-catheterizations were used to evaluate functional outcomes in the baseline and 1 year after operation. RESULTS: There were better physical and social functioning scales, less fatigue symptoms, better IIEF (16 versus 3.7, p = 0.01), and less self-catheterization rate (33% versus 89%  p = 0.006) in the PSC group. The oncologic outcomes were the same between two groups. CONCLUSIONS: For selected patients with bladder cancer who underwent neobladder reconstruction, prostate-sparing cystectomy provided better sexuality preservation, less daily self-catheterization, and better physical function and social function scales without compromising overall survival.	bladder
Semiparametric regression analysis of failure time data with dependent interval censoring.	Interval-censored failure-time data arise when subjects are examined or observed periodically such that the failure time of interest is not examined exactly but only known to be bracketed between two adjacent observation times. The commonly used approaches assume that the examination times and the failure time are independent or conditionally independent given covariates. In many practical applications, patients who are already in poor health or have a weak immune system before treatment usually tend to visit physicians more often after treatment than those with better health or immune system. In this situation, the visiting rate is positively correlated with the risk of failure due to the health status, which results in dependent interval-censored data. While some measurable factors affecting health status such as age, gender, and physical symptom can be included in the covariates, some health-related latent variables cannot be observed or measured. To deal with dependent interval censoring involving unobserved latent variable, we characterize the visiting/examination process as recurrent event process and propose a joint frailty model to account for the association of the failure time and visiting process. A shared gamma frailty is incorporated into the Cox model and proportional intensity model for the failure time and visiting process, respectively, in a multiplicative way. We propose a semiparametric maximum likelihood approach for estimating model parameters and show the asymptotic properties, including consistency and weak convergence. Extensive simulation studies are conducted and a data set of bladder cancer is analyzed for illustrative purposes. Copyright © 2017 John Wiley & Sons, Ltd.	bladder
Concurrent chemotherapy is associated with improved survival in elderly patients with bladder cancer undergoing radiotherapy.	BACKGROUND: The current study was conducted to compare the overall survival (OS) of concurrent chemoradiotherapy (CCRT) versus radiotherapy (RT) alone in elderly patients (those aged ≥80 years) with muscle-invasive bladder cancer (MIBC). METHODS: Patients aged ≥80 years with cT2-4, N0-3, M0 transitional cell MIBC who were treated with curative RT (60-70 Gray) or CCRT were identified in the National Cancer Data Base. Univariable and multivariable frailty survival analyses, as well as 1-to-1 propensity score matching, were used to isolate the association between CCRT and OS. RESULTS: A total of 1369 patients who were treated with RT from 2004 through 2013 met eligibility criteria: 739 patients (54%) received RT alone and 630 patients (46%) received CCRT. The median age of the patients was 84 years (range, 80-90 years). The median follow-up was 21 months. The 2-year OS rate was 48%. When comparing CCRT with RT alone, the 2-year OS rate was 56% versus 42% (P<.0001), respectively. Multivariable analysis demonstrated that CCRT (hazard ratio [HR], 0.74; 95% confidence interval [95% CI], 0.65-0.84 [P<.0001]) and a higher RT dose (HR, 0.78; 95% CI, 0.67-0.90 [P<.001]) were associated with improved OS. T4 disease was associated with worse OS (HR, 1.42; 95% CI, 1.15-1.76 [P = .001]). After using 1-to-1 propensity score matching, there remained an OS benefit for the use of CCRT (HR, 0.77; 95% CI, 0.67-0.90 [P<.001]). CONCLUSIONS: CCRT is associated with improved OS compared with the use of RT alone in elderly patients with MIBC, independent of Charlson-Deyo comorbidity score, suggesting that CCRT should be used in this population. Cancer 2017;123:3524-31. © 2017 American Cancer Society.	bladder
Updates for the radiologist in non-muscle-invasive, muscle-invasive, and metastatic bladder cancer.	Urothelial bladder cancer is a common malignancy requiring a multidisciplinary approach to treatment. Significant recent advances have been made in terms of the genetic and molecular characterization of bladder cancer subtypes, and novel treatment approaches are being investigated and approved. Given the important role of imaging in the diagnosis, staging, and follow-up of this disease, it is necessary for radiologists to remain up-to-date in terms of nomenclature and standards of care. In this review, recent developments in bladder cancer characterization and treatment will be discussed, with reference to the contributions of imaging in non-muscle-invasive, muscle-invasive, and metastatic settings.	bladder
Preoperative Prognostic Nutritional Index is a Significant Predictor of Survival with Bladder Cancer after Radical Cystectomy: a retrospective study.	BACKGROUND: To explore the prognostic significance of preoperative prognostic nutritional index (PNI) in bladder cancer after radical cystectomy and compare the prognostic ability of inflammation-based indices. METHODS: We retrospectively analyzed data for 516 patients with bladder cancer who underwent radical cystectomy in our institution between 2006 to 2012. Clinicopathologic characteristics and inflammation-based indices (PNI, neutrophil/lymphocyte ratio [NLR], platelet/lymphocyte ratio [PLR], lymphocyte/monocyte ratio [LMR]) were evaluated by pre-treatment measurements. Overall survival (OS) and progression-free survival (PFS) were estimated by the Kaplan-Meier method and compared by log-rank test. Multivariate analysis with a Cox proportional hazards model was used to confirm predictors identified on univariate analysis. The association between clinicopathological characteristics and PNI or NLR was tested. RESULTS: Among the 516 patients, the median follow-up was 37 months (interquartile range 20 to 56). On multivariate analysis, PNI and NLR independently predicted OS (PNI: hazard ratio [HR] = 1.668, 95% CI: 1.147-2.425, P = 0.007; NLR: HR = 1.416, 95% CI:1.094-2.016, P = 0.0149) and PFS (PNI: HR = 1.680, 95% CI:1.092-2.005, P = 0.015; NLR: HR = 1.550, 95% CI:1.140-2.388, P = 0.008). Low PNI predicted worse OS for all pathological stages and PFS for T1 and T2 stages. Low PNI was associated with older age (>65 years), muscle-invasive bladder cancer, high American Society of Anesthesiologists grade and anemia. CONCLUSION: PNI and NLR were independent predictors of OS and PFS for patients with bladder cancer after radical cystectomy and PNI might be a novel reliable biomarker for bladder cancer.	bladder
Healthcare-Associated Mycobacterium bovis-Bacille Calmette-Guérin (BCG) Infection in Cancer Patients Without Prior BCG Instillation.	BACKGROUND: Bacille Calmette-Guérin (BCG), an attenuated strain of Mycobacterium bovis, is widely used as adjunctive therapy for superficial bladder cancer. Intravesical administration of BCG has been associated with systemic infection. Disseminated infection due to M. bovis is otherwise uncommon. METHODS: After identification of 3 patients with healthcare-associated BCG infection who had never received intravesical BCG administration, an epidemiologic study was performed. All patients with healthcare-associated BCG infection in the Barcelona tuberculosis (TB) program were reviewed from 1 January 2005 to 31 December 2015, searching for infections caused by M. bovis-BCG. Patients with healthcare-associated BCG infection who had not received intravesical BCG instillation were selected and the source of infection was investigated. RESULTS: Nine oncology patients with infection caused by M. bovis-BCG were studied. All had permanent central venous catheters. Catheter maintenance was performed at 4 different outpatient clinics in the same room in which other patients underwent BCG instillations for bladder cancer without required biological precautions. All patients developed pulmonary TB, either alone or with extrapulmonary disease. Catheter-related infection was considered the mechanism of acquisition based on the epidemiologic association and positive catheter cultures for BCG in patients in whom mycobacterial cultures were performed. CONCLUSIONS: Physicians should be alerted to the possibility of TB due to nosocomially acquired, catheter-related infections with M. bovis-BCG in patients with indwelling catheters. This problem may be more common than expected in centers providing BCG therapy for bladder cancer without adequate precautions.	bladder
Nelfinavir and Ritonavir Kill Bladder Cancer Cells Synergistically by Inducing Endoplasmic Reticulum Stress.	The human immunodeficiency virus (HIV) protease inhibitor nelfinavir acts against malignancies by inducing endoplasmic reticulum (ER) stress. The HIV protease inhibitor ritonavir, on the other hand, not only induces ER stress but also inhibits P-glycoprotein's pump activity and thereby enhances the effects of its substrate drugs. We therefore postulated that ritonavir in combination with nelfinavir would kill bladder cancer cells effectively by inducing ER stress cooperatively and also enhancing nelfinavir's effect. Nelfinavir was shown to be a P-glycoprotein substrate, and the combination of nelfinavir and ritonavir inhibited bladder cancer cell growth synergistically. It also suppressed colony formation significantly. The combination significantly increased the number of cells in the sub-G1 fraction and also the number of annexin V+ cells, confirming robust apoptosis induction. The combination induced ER stress synergistically, as evidenced by the increased expression of glucose-regulated protein 78, ER-resident protein 44, and endoplasmic oxidoreductin-1-like protein. It also increased the expression of the mammalian target of rapamycin (mTOR) inhibitor AMP-activated protein kinase and caused dephosphorylation of S6 ribosomal protein, demonstrating that the combination also inhibited the mTOR pathway. We also found that the combination enhanced histone acetylation synergistically by decreasing the expression of HDACs 1, 3, and 6.	bladder
Ten-Year Review of Perioperative Complications After Transurethral Resection of Bladder Tumors: Analysis of Monopolar and Plasmakinetic Bipolar Cases.	OBJECTIVES: To evaluate the rate of perioperative complications after plasmakinetic bipolar and monopolar transurethral resection of bladder tumor (BTURB and MTURB). In addition, the study identifies patient and procedure characteristics associated with early complications. PATIENTS AND METHODS: Retrospective review was conducted on patients undergoing transurethral resection of bladder tumor procedures at a single institution from 2003 to 2013 to assess the 30-day complication rates associated with BTURB and MTURB. RESULTS: Four hundred twenty-seven patients met inclusion criteria and underwent 586 procedures (379 BTURB and 207 MTURB). Baseline patient demographics, tumor stage, and tumor grade were similar in BTURB and MTURB cohorts. The overall complication rate was 34.3% for MTURB and 26.7% for BTURB. The most frequent complications were acute urinary retention (AUR) 11%, hematuria 8%, and urinary tract infection (UTI) 7%. There was no statistical difference in rates of AUR, hematuria, UTI, or readmission for continuous bladder irrigation or hemostasis procedures between BTURB and MTURB cohorts. There was a trend toward lower perforation rate during BTURB (2.6% vs 5.8%). In multivariate logistic regression analysis, MTURB, male gender, and large resections were predictive of overall complications. Male gender was associated with hematuria and AUR. Large bladder tumor resection size was also associated with increased risk of overall complications and AUR. CONCLUSION: BTURB was associated with a lower risk of overall complications, but there was no difference in the rate of hematuria in the two cohorts. Male gender and large tumor size are associated with higher risk of early complications.	bladder
Correlations of Foxo3 and Foxo4 expressions with clinicopathological features and prognosis of bladder cancer.	OBJECTIVE: The study is performed to explore the correlations of forkhead box O3 (FoxO3) and forkhead box O4 (FoxO4) expressions with clinicopathological features and prognosis of bladder cancer. METHODS: Bladder cancer tissues and adjacent normal tissues from the recruited 222 patients were collected. Quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting and immunohistochemistry were applied to determine the expressions of FoxO3 and FoxO4. Spearman correlation analysis was conducted to examine the correlation between the expressions of FoxO3 and FoxO4. All patients were followed up and overall survival (OS) and disease-free survival (DFS) were recorded. Kaplan-Meier survival curve was drawn to determine the associations of FoxO3 and FoxO4 expressions and postoperative survival. Cox proportional hazards model was conducted to analyze the risk factors for poor prognosis of bladder cancer. RESULTS: The mRNA and expressions of FoxO3 and FoxO4 proteins in the bladder cancer tissues were lower than that in the adjacent normal tissues (both P<0.05). The positive rates of FoxO3 and FoxO4 were lower in the patients with lymph node metastasis than that in the patients without lymph node metastasis (P<0.05), and significantly lower in the patients with non-muscle invasive bladder cancer (T(is)-T(1)) than in those with non-muscle invasive bladder cancer (T(2)-T(3)) in TNM staging, and remarkably lower in the patients with high grade than in those with low grade in the histological type (P<0.05). Furthermore, the expressions of FoxO3 and FoxO4 were positively correlated in the bladder cancer tissues (P<0.05). Negative expressions of FoxO3 and FoxO4 and lymph node metastasis were the risk factors for the poor prognosis of bladder cancer. CONCLUSIONS: The FoxO3 and FoxO4 expressions may potentially associate with the clinicopathological features and prognosis of bladder cancer.	bladder
Mass spectrometric detection combined with bioinformatic analysis identified possible protein markers and key pathways associated with bladder cancer.	We aimed to find possible protein markers and key pathways related to bladder cancer. In total, we extracted three bladder cancer tissues and three paracancerous tissues from Jiangsu Provincial People's Hospital Urology Department, and performed mass spectrometric detection with Q Exactive. Subsequently, we screened the differentially expressed proteins in the disease group and the normal group using the LIMMA package, and performed functional enrichment analyses using DAVID. Further, we constructed protein-protein interaction (PPI) networks with Cytoscape software, and analyzed modules with ClusterONE. In total, 165 differentially expressed proteins including 19 upregulated and 146 downregulated ones were obtained. ACTA2 (Actin, Alpha 2, Smooth Muscle, Aorta), ACTN1 (Actinin, Alpha 1), and VCL (Vinculin) were significant nodes with higher degrees in the PPI network. These three nodes were also hub nodes in module 2. Besides, functional enrichment analysis suggested that ECM-receptor interaction and focal adhesion were significant pathways, and these two pathways were also enriched in three network modules. In addition, ACTN1 and VCL were enriched in the focal adhesion pathway in module 2. Thus, ACTA2, ACTN1, and VCL may play important roles in bladder cancer progression and may be protein markers for this disease. The ECM-receptor interaction pathway and the focal adhesion pathway may be involved in the progression of bladder cancer. Furthermore, ACTN1 and VCL may play roles in bladder cancer development, partly via the focal adhesion pathway.	bladder